pychemcurv.vis

The pychemcurv.vis module implements the CurvatureViewer class in order to visualize a molecule or a periodic structure in a jupyter notebook and map a given properties on the atoms using a color scale.

This class needs, nglview and uses ipywidgets in a jupyter notebook to display the visualization. Run the following instructions to install nglview and achieve the configuration in order to be able to use nglview in a jupyter notebook

conda install nglview -c conda-forge
jupyter-nbextension enable nglview --py --sys-prefix

or

pip install nglview
jupyter-nbextension enable nglview --py --sys-prefix

Visualization of the pyramidalization angle using a color scale.

CurvatureViewer class

class pychemcurv.vis.CurvatureViewer(structure, bond_tol=0.2, rcut=2.5, bond_order=None)

This class provides a constructor for a NGLView widget in order to visualize the wanted properties using a color scale mapped on the 3D structure of the molecule or the structure.

The class needs a pymatgen.Structure or pymatgen.Molecule object as first argument. The other arguments are used to defined if two atoms are bonded or not.

Parameters

• structure (Structure, Molecule) – A Structure or Molecule pymatgen objects

• bond_tol (float) – Tolerance used to determine if two atoms are bonded. Look at pymatgen.core.CovalentBond.is_bonded.

• rcut (float) – Cutoff distance in case the bond is not not known

• bond_order (dict) – Not yet implemented

get_view(representation='ball+stick', radius=0.25, aspect_ratio=2, unitcell=False, width='700px', height='500px')

Set up a simple NGLView widget with the ball and stick or licorice representation of the structure.

Parameters

• representation (str) – representation: ‘ball+stick’ or ‘licorice’

• radius (float) – bond (stick) radius

• aspect_ratio (float) – ratio between the balls and stick radiuses

• unitcell (bool) – If True and structure is periodic, show the unitcell.

• width (str) – width of the nglview widget, default ‘700px’

• height (str) – height of the nglview widget, default ‘500px’

Returns

Return a NGLWidget object

map_view(prop, radius=0.25, aspect_ratio=2, unitcell=False, cm='viridis', minval=None, maxval=None, orientation='vertical', label=None, width='700px', height='500px')

Map the given properties on a color scale on to the molecule using a ball and stick representations. The properties can be either the name of a column of the data computed using the CurvatureAnalyzer class, or, an array of values of a custum property. In the last case, the size of the array must be consistent with the number of atoms in the system.

Parameters

• prop (str or array) – name of the properties or values you want to map

• radius (float) – bond (stick) radius

• aspect_ratio (float) – ratio between the balls and stick radiuses

• unitcell (bool) – If True and structure is periodic, show the unitcell.

• cm (str) – colormap from matplotlib.cm.

• minval (float) – minimum value to consider for the color sacle

• maxval (float) – maximum value to consider for the color sacle

• orientation (str) – orientation of the colorbar 'horizontal' or 'vertical'

• label (str) – Name of the colorbar. If None, use prop.

• width (str) – width of the nglview widget, default ‘700px’

• height (str) – height of the nglview widget, default ‘500px’

Returns

Returns an ipywidgets HBox or VBox with the NGLWidget and a color bar associated to the mapped properties. The NGLWidget is the first element of the children, the colorbar is the second one.